Just to confirm that the corresponding Law n.º 23/2007 was amended back in 2015:
https://dre.pt/dre/legislacao-consolidada/lei/2007-67564445-155563978
It is indeed 90 days now for the initial grant, and then 60 days for renewals.
(Funny that SEF’s own manual dated 2017 still refers to 60 days, two years after the Law was amended… 
)